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Chlorine in PDB 2afv: The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis

Enzymatic activity of The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis

All present enzymatic activity of The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis:
5.4.1.2;

Protein crystallography data

The structure of The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis, PDB code: 2afv was solved by Y.Xue, Z.Wei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 3.00
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 113.078, 113.078, 114.502, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis (pdb code 2afv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis, PDB code: 2afv:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 2afv

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Chlorine binding site 1 out of 8 in the The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1003

b:22.9
occ:1.00
 N A:SER172 3.0 29.8 1.0
N A:VAL171 3.2 30.9 1.0
N A:PHE170 3.6 28.8 1.0
CB A:VAL171 3.6 30.1 1.0
CG A:PRO143 3.7 31.4 1.0
CA A:VAL171 3.7 29.8 1.0
N A:ALA173 3.7 28.9 1.0
C A:VAL171 3.8 30.2 1.0
CA A:GLY169 3.9 28.8 1.0
CA A:SER172 4.0 28.6 1.0
CG2 B:ILE14 4.0 27.8 1.0
CD A:PRO143 4.1 31.9 1.0
C A:GLY169 4.2 28.6 1.0
C A:SER172 4.2 29.1 1.0
CB A:SER172 4.2 26.5 1.0
C A:PHE170 4.3 31.5 1.0
CB A:PRO143 4.4 31.5 1.0
CA A:PHE170 4.5 30.4 1.0
CG2 A:VAL171 4.5 30.4 1.0
OG A:SER172 4.6 26.1 1.0
CA A:ALA173 4.7 28.4 1.0
CG1 A:VAL171 4.7 31.7 1.0
CB A:ALA173 4.7 27.2 1.0
O A:VAL171 5.0 32.2 1.0

Chlorine binding site 2 out of 8 in 2afv

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Chlorine binding site 2 out of 8 in the The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1004

b:39.6
occ:1.00
 OG1 A:THR144 2.8 29.7 1.0
CG2 A:THR144 3.2 26.8 1.0
CD A:PRO143 3.4 31.9 1.0
CB A:THR144 3.5 27.6 1.0
N A:THR144 3.5 27.6 1.0
CB A:ALA142 3.6 34.5 1.0
CA A:ALA142 3.6 33.3 1.0
N A:PRO143 3.7 32.4 1.0
C A:ALA142 3.9 33.5 1.0
CA A:THR144 4.1 27.1 1.0
CD1 B:ILE14 4.4 26.8 1.0
C A:PRO143 4.5 29.7 1.0
CA A:PRO143 4.6 30.9 1.0
CG A:PRO143 4.7 31.4 1.0
O A:ALA142 4.8 34.5 1.0
CB A:PRO143 4.8 31.5 1.0
CG2 A:THR117 4.8 45.6 1.0
OG1 A:THR117 4.8 47.0 1.0
N A:ALA142 5.0 34.5 1.0

Chlorine binding site 3 out of 8 in 2afv

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Chlorine binding site 3 out of 8 in the The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1005

b:23.6
occ:0.75
 OG A:SER30 3.1 40.2 1.0
N A:SER30 3.2 38.4 1.0
CA A:HIS29 3.7 37.8 1.0
CB A:HIS29 3.8 36.7 1.0
CE A:LYS52 3.9 34.5 1.0
CE1 A:PHE31 4.0 34.6 1.0
CB A:SER30 4.0 38.4 1.0
C A:HIS29 4.0 38.2 1.0
O A:LYS52 4.1 25.1 1.0
CA A:SER30 4.2 38.4 1.0
CD1 A:PHE31 4.4 35.0 1.0
CG A:LYS52 4.6 29.6 1.0
CZ A:PHE31 4.8 34.7 1.0
CD A:LYS52 4.8 32.5 1.0
NZ A:LYS52 4.9 37.0 1.0
C A:SER30 4.9 38.2 1.0
O A:PRO28 5.0 39.0 1.0

Chlorine binding site 4 out of 8 in 2afv

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Chlorine binding site 4 out of 8 in the The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1007

b:34.3
occ:0.75
 OG A:SER203 3.1 25.8 1.0
N A:SER203 3.3 25.6 1.0
CA A:GLY202 3.8 28.5 1.0
CB A:SER203 3.9 24.2 1.0
OG1 B:THR204 4.0 29.8 1.0
C A:GLY202 4.1 26.9 1.0
CG2 B:THR204 4.1 31.6 1.0
O A:GLY140 4.1 33.1 1.0
CA A:SER203 4.2 24.9 1.0
CB A:ASN141 4.4 38.7 1.0
CG A:ASN141 4.5 42.5 1.0
CE A:MET81 4.6 53.4 1.0
CB B:THR204 4.7 29.1 1.0
CG1 A:VAL168 4.8 28.6 1.0
OD1 A:ASN141 4.8 43.0 1.0
ND2 A:ASN141 4.9 45.1 1.0
O B:ALA45 5.0 22.5 1.0

Chlorine binding site 5 out of 8 in 2afv

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Chlorine binding site 5 out of 8 in the The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1001

b:35.2
occ:1.00
 OG1 B:THR144 3.0 20.6 1.0
CD B:PRO143 3.2 25.9 1.0
CG2 B:THR144 3.2 17.5 1.0
N B:THR144 3.2 22.5 1.0
N B:PRO143 3.3 26.5 1.0
CB B:THR144 3.6 20.0 1.0
CA B:ALA142 3.6 28.4 1.0
CB B:ALA142 3.6 27.8 1.0
C B:ALA142 3.7 27.3 1.0
CA B:THR144 4.0 22.0 1.0
C B:PRO143 4.2 24.0 1.0
CA B:PRO143 4.2 25.2 1.0
CG B:PRO143 4.4 25.1 1.0
CB B:PRO143 4.4 24.6 1.0
O B:ALA142 4.6 27.1 1.0
CD1 A:ILE14 4.7 28.0 1.0
N B:ALA145 4.9 21.9 1.0
O B:ASN141 4.9 35.0 1.0
N B:ALA142 4.9 31.1 1.0

Chlorine binding site 6 out of 8 in 2afv

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Chlorine binding site 6 out of 8 in the The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1002

b:29.5
occ:1.00
 N B:SER172 3.1 25.1 1.0
N B:VAL171 3.2 24.8 1.0
CB B:VAL171 3.6 20.2 1.0
N B:ALA173 3.6 23.2 1.0
CG B:PRO143 3.7 25.1 1.0
N B:PHE170 3.7 23.6 1.0
CA B:GLY169 3.7 25.1 1.0
CA B:VAL171 3.7 23.3 1.0
C B:VAL171 3.9 25.1 1.0
C B:GLY169 4.0 24.2 1.0
CA B:SER172 4.1 24.4 1.0
CG2 A:ILE14 4.1 32.9 1.0
CD B:PRO143 4.1 25.9 1.0
CG2 B:VAL171 4.2 19.5 1.0
C B:SER172 4.3 24.1 1.0
CB B:PRO143 4.4 24.6 1.0
C B:PHE170 4.4 25.4 1.0
CB B:SER172 4.4 25.2 1.0
CB B:ALA173 4.4 21.0 1.0
CA B:ALA173 4.5 21.6 1.0
CA B:PHE170 4.6 24.3 1.0
CG1 B:VAL171 4.9 19.1 1.0
N B:GLY169 4.9 23.8 1.0
OG B:SER172 4.9 27.8 1.0
O B:VAL168 5.0 23.6 1.0
O B:GLY169 5.0 23.3 1.0
OG A:SER18 5.0 30.1 1.0

Chlorine binding site 7 out of 8 in 2afv

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Chlorine binding site 7 out of 8 in the The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1006

b:40.1
occ:0.75
 N B:SER30 3.1 42.2 1.0
OG B:SER30 3.1 40.0 1.0
CA B:HIS29 3.6 42.4 1.0
CB B:HIS29 3.7 42.7 1.0
C B:HIS29 3.7 42.1 1.0
CB B:SER30 3.7 40.3 1.0
CE1 B:PHE31 3.8 40.2 1.0
CA B:SER30 4.0 42.0 1.0
O B:LYS52 4.1 24.7 1.0
CE B:LYS52 4.1 28.9 1.0
CD1 B:PHE31 4.3 39.4 1.0
CZ B:PHE31 4.6 39.3 1.0
CG B:LYS52 4.7 25.7 1.0
C B:SER30 4.8 42.2 1.0
O B:HIS29 4.9 43.6 1.0
CG B:HIS29 5.0 42.4 1.0

Chlorine binding site 8 out of 8 in 2afv

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Chlorine binding site 8 out of 8 in the The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1008

b:39.1
occ:0.75
 OG B:SER203 3.1 27.9 1.0
N B:SER203 3.4 28.0 1.0
CG B:ASN141 3.7 38.0 1.0
ND2 B:ASN141 3.8 41.8 1.0
CB B:ASN141 3.9 34.2 1.0
O B:GLY140 3.9 32.7 1.0
CA B:GLY202 3.9 27.3 1.0
OD1 B:ASN141 4.0 39.2 1.0
CB B:SER203 4.0 26.6 1.0
C B:GLY202 4.2 27.2 1.0
CE B:MET81 4.2 51.9 1.0
CA B:SER203 4.3 27.4 1.0
CG1 B:VAL168 4.4 24.2 1.0
CA B:ASN141 4.5 33.1 1.0
OG1 A:THR204 4.5 24.7 1.0
O A:HOH1036 4.7 35.9 1.0
C B:GLY140 4.7 31.5 1.0

Reference:

Y.Xue, Z.Wei, X.Li, W.Gong. The Crystal Structure of Putative Precorrin Isomerase Cbic in Cobalamin Biosynthesis J.Struct.Biol. V. 153 307 2006.
ISSN: ISSN 1047-8477
PubMed: 16427313
DOI: 10.1016/J.JSB.2005.11.011
Page generated: Thu Jul 10 21:07:42 2025

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